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Bulk and single-cell RNA sequencing reveal the roles of neutrophils in pediatric Crohn’s disease

Pediatric Research volume 98, pages 1950–1959 (2025)Cite this article

Abstract

Background

Pediatric Crohn’s disease (CD) is a chronic inflammatory bowel disorder that poses significant health risks to children. Although the precise etiology of CD remains elusive, further exploration is needed to identify diagnostic biomarkers and therapeutic targets.

Methods

This study utilized single-cell and bulk RNA sequencing data derived from ileal and colonic biopsy samples to explore the molecular mechanisms and cell types associated with CD, as well as to pinpoint potential biomarkers and therapeutic targets.

Results

The results revealed a more pronounced alteration in both the quantity and functional state of neutrophils in the CD cohort compared to those with ulcerative colitis and healthy controls. Neutrophils were present in higher proportions in the CD group, primarily in an activated state, potentially correlating with the presence of deep ulcerations and inflammatory histopathological features. Additionally, neutrophil interactions with other cell types were markedly enhanced in the CD group, making neutrophils the dominant participants in cell-to-cell communications. Further analysis indicated a shift in neutrophil phenotype from pro-inflammatory and antimicrobial to tissue-repairing, which may contribute to the progression and exacerbation of CD.

Conclusion

IL1B, ICAM1, CXCL1, and CXCL9, primarily expressed in neutrophils, were potential biomarkers for CD. Neutrophils might be considered a potential target for pediatric CD.

Impact Statement

  • This study demonstrated that patients with CD exhibited a greater proportion of activated neutrophils, with enhanced interactions between neutrophils and all other cell types, resulting in neutrophils contributing the most cell-cell interactions within the CD gut.

  • Neutrophils in the CD gut transition from a pro-inflammatory and antibacterial phenotype to one that promotes tissue healing, potentially influencing the progression and exacerbation of CD. Neutrophils represent a promising therapeutic target in pediatric CD.

  • Hub genes associated with CD, including IL1B, ICAM1, CXCL1, and CXCL9, are predominantly expressed in neutrophils, positioning them as promising diagnostic biomarkers for CD.

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Fig. 1: WGCNA identified gene coexpression modules associated with CD.
Fig. 2: Identification of independent risk/protective genes related to CD.
Fig. 3: Construction and verification of a nomogram for the diagnosis of CD.
Fig. 4: scRNA-seq data revealed neutrophil populations related to CD.
Fig. 5: Neutrophil reclustering and subcluster analysis.
Fig. 6: Immunological characteristics related to CD.

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Data availability

Data supporting our research can be obtained from the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/). The data generated during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

The authors sincerely acknowledge the study participants who donated the samples. The study was supported by the Youth Program of the National Natural Science Foundation of China (No. 81902439).

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Authors and Affiliations

  1. Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China

    Lei Xu & Biao Zou

  2. Department of Ultrasonography, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China

    Ting Xiao

  3. Department of Nursing, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China

    Ling Xu

  4. Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China

    Wei Yao

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  1. Lei Xu
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  2. Ting Xiao
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Contributions

L.X. and T.X. conceived the idea, designed the study, analyzed data, performed most of the experiments, and drafted the manuscript. L.X. and B.Z. assisted in designing the study, data analysis, drafting the manuscript, and sample collection. Y.W. supervised the entire project.

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Correspondence to Biao Zou or Wei Yao.

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Xu, L., Xiao, T., Xu, L. et al. Bulk and single-cell RNA sequencing reveal the roles of neutrophils in pediatric Crohn’s disease. Pediatr Res 98, 1950–1959 (2025). https://doi.org/10.1038/s41390-025-03961-x

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